Structure

Physi-Chem Properties

Molecular Weight:  363.35
Volume:  435.538
LogP:  8.285
LogD:  4.909
LogS:  -5.128
# Rotatable Bonds:  19
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.2
Synthetic Accessibility Score:  2.485
Fsp3:  0.792
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.849
MDCK Permeability:  9.812556527322158e-06
Pgp-inhibitor:  0.003
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.454
30% Bioavailability (F30%):  0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.165
Plasma Protein Binding (PPB):  98.68643951416016%
Volume Distribution (VD):  1.459
Pgp-substrate:  1.851727843284607%

ADMET: Metabolism

CYP1A2-inhibitor:  0.137
CYP1A2-substrate:  0.223
CYP2C19-inhibitor:  0.448
CYP2C19-substrate:  0.392
CYP2C9-inhibitor:  0.2
CYP2C9-substrate:  0.955
CYP2D6-inhibitor:  0.503
CYP2D6-substrate:  0.17
CYP3A4-inhibitor:  0.736
CYP3A4-substrate:  0.132

ADMET: Excretion

Clearance (CL):  4.001
Half-life (T1/2):  0.183

ADMET: Toxicity

hERG Blockers:  0.77
Human Hepatotoxicity (H-HT):  0.517
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.078
Maximum Recommended Daily Dose:  0.672
Skin Sensitization:  0.981
Carcinogencity:  0.073
Eye Corrosion:  0.084
Eye Irritation:  0.668
Respiratory Toxicity:  0.964

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC104138

Natural Product ID:  NPC104138
Common Name*:   (2E,4E)-N-Isobutyleicosa-2,4-Dienamide
IUPAC Name:   (2E,4E)-N-(2-methylpropyl)icosa-2,4-dienamide
Synonyms:  
Standard InCHIKey:  LMZPUHBJSQVRHE-HYGARKJASA-N
Standard InCHI:  InChI=1S/C24H45NO/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-24(26)25-22-23(2)3/h18-21,23H,4-17,22H2,1-3H3,(H,25,26)/b19-18+,21-20+
SMILES:  CCCCCCCCCCCCCCC/C=C/C=C/C(=NCC(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2347638
PubChem CID:   6441067
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[16872768]
NPO26237 Piper longum Species Piperaceae Eukaryota fruits n.a. n.a. PMID[20839888]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[23434420]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2 Others Unspecified Ratio CC50/IC50 = 1.5 n.a. PMID[533963]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 1070000.0 nM PMID[533963]
NPT2 Others Unspecified Ratio CC50/IC50 = 2.7 n.a. PMID[533963]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 580000.0 nM PMID[533963]
NPT27 Others Unspecified CC50 = 1580000.0 nM PMID[533963]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC104138 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC261158
1.0 High Similarity NPC306420
1.0 High Similarity NPC24216
0.9808 High Similarity NPC297020
0.9808 High Similarity NPC273023
0.9423 High Similarity NPC303672
0.9231 High Similarity NPC195986
0.9107 High Similarity NPC312826
0.9074 High Similarity NPC471992
0.9038 High Similarity NPC54542
0.9038 High Similarity NPC267340
0.9038 High Similarity NPC145032
0.9038 High Similarity NPC243539
0.9038 High Similarity NPC304223
0.8846 High Similarity NPC267692
0.8846 High Similarity NPC307435
0.8727 High Similarity NPC471991
0.8704 High Similarity NPC119655
0.8545 High Similarity NPC163912
0.8545 High Similarity NPC305288
0.8545 High Similarity NPC167759
0.8545 High Similarity NPC56028
0.8305 Intermediate Similarity NPC6795
0.8246 Intermediate Similarity NPC477049
0.8226 Intermediate Similarity NPC187315
0.8214 Intermediate Similarity NPC246519
0.8214 Intermediate Similarity NPC132669
0.8214 Intermediate Similarity NPC14234
0.8214 Intermediate Similarity NPC269800
0.8214 Intermediate Similarity NPC184014
0.8214 Intermediate Similarity NPC13011
0.8214 Intermediate Similarity NPC44193
0.8214 Intermediate Similarity NPC124382
0.8214 Intermediate Similarity NPC123669
0.8065 Intermediate Similarity NPC477525
0.8 Intermediate Similarity NPC130807
0.7931 Intermediate Similarity NPC4881
0.7705 Intermediate Similarity NPC309877
0.7581 Intermediate Similarity NPC29468
0.75 Intermediate Similarity NPC245650
0.746 Intermediate Similarity NPC471023
0.7455 Intermediate Similarity NPC91044
0.7385 Intermediate Similarity NPC315141
0.7385 Intermediate Similarity NPC129995
0.7302 Intermediate Similarity NPC324077
0.7188 Intermediate Similarity NPC182758
0.7164 Intermediate Similarity NPC249713
0.7077 Intermediate Similarity NPC235311
0.7077 Intermediate Similarity NPC253468
0.7 Intermediate Similarity NPC314678
0.6984 Remote Similarity NPC150505
0.6984 Remote Similarity NPC329003
0.6984 Remote Similarity NPC74617
0.6984 Remote Similarity NPC326524
0.6984 Remote Similarity NPC325550
0.6923 Remote Similarity NPC77891
0.6885 Remote Similarity NPC242930
0.6825 Remote Similarity NPC210999
0.6825 Remote Similarity NPC321030
0.6812 Remote Similarity NPC45060
0.6812 Remote Similarity NPC471022
0.6812 Remote Similarity NPC103712
0.6812 Remote Similarity NPC291196
0.6812 Remote Similarity NPC280065
0.678 Remote Similarity NPC261571
0.6727 Remote Similarity NPC86121
0.6727 Remote Similarity NPC470439
0.6667 Remote Similarity NPC188341
0.6667 Remote Similarity NPC208638
0.6667 Remote Similarity NPC49494
0.6667 Remote Similarity NPC316674
0.6623 Remote Similarity NPC14326
0.6607 Remote Similarity NPC138935
0.6562 Remote Similarity NPC325734
0.6515 Remote Similarity NPC273614
0.6438 Remote Similarity NPC288086
0.6379 Remote Similarity NPC180575
0.6333 Remote Similarity NPC26960
0.6333 Remote Similarity NPC182102
0.6207 Remote Similarity NPC299114
0.6207 Remote Similarity NPC269074
0.6203 Remote Similarity NPC224072
0.6203 Remote Similarity NPC39966
0.6176 Remote Similarity NPC55068
0.6173 Remote Similarity NPC3210
0.6133 Remote Similarity NPC476923
0.6119 Remote Similarity NPC176621
0.6094 Remote Similarity NPC474644
0.6094 Remote Similarity NPC329686
0.6071 Remote Similarity NPC269823
0.6066 Remote Similarity NPC249670
0.6066 Remote Similarity NPC473913
0.6066 Remote Similarity NPC474642
0.6024 Remote Similarity NPC473031
0.6 Remote Similarity NPC55412
0.6 Remote Similarity NPC473865
0.6 Remote Similarity NPC474643
0.6 Remote Similarity NPC15934
0.6 Remote Similarity NPC249645
0.5968 Remote Similarity NPC473672
0.5968 Remote Similarity NPC474495
0.5968 Remote Similarity NPC59408
0.5968 Remote Similarity NPC71053
0.5965 Remote Similarity NPC206906
0.5965 Remote Similarity NPC256766
0.5965 Remote Similarity NPC213538
0.5952 Remote Similarity NPC316186
0.5942 Remote Similarity NPC477106
0.5921 Remote Similarity NPC476924
0.5904 Remote Similarity NPC203076
0.5902 Remote Similarity NPC248884
0.5902 Remote Similarity NPC85079
0.5902 Remote Similarity NPC31194
0.5897 Remote Similarity NPC473446
0.5897 Remote Similarity NPC473695
0.5875 Remote Similarity NPC82799
0.5862 Remote Similarity NPC116934
0.5833 Remote Similarity NPC19834
0.5833 Remote Similarity NPC55063
0.5823 Remote Similarity NPC313911
0.5823 Remote Similarity NPC314854
0.5806 Remote Similarity NPC72699
0.5806 Remote Similarity NPC477727
0.5806 Remote Similarity NPC199286
0.5806 Remote Similarity NPC471281
0.5797 Remote Similarity NPC469728
0.5783 Remote Similarity NPC152684
0.5781 Remote Similarity NPC34577
0.5781 Remote Similarity NPC61177
0.5775 Remote Similarity NPC308844
0.575 Remote Similarity NPC476560
0.5714 Remote Similarity NPC29091
0.5714 Remote Similarity NPC182840
0.5714 Remote Similarity NPC217095
0.5714 Remote Similarity NPC329608
0.5714 Remote Similarity NPC224148
0.5714 Remote Similarity NPC170776
0.5714 Remote Similarity NPC9273
0.5714 Remote Similarity NPC76198
0.5714 Remote Similarity NPC166458
0.5714 Remote Similarity NPC151782
0.5714 Remote Similarity NPC264417
0.5714 Remote Similarity NPC471959
0.5714 Remote Similarity NPC103213
0.5714 Remote Similarity NPC475477
0.5714 Remote Similarity NPC89824
0.5714 Remote Similarity NPC294278
0.5714 Remote Similarity NPC197272
0.5714 Remote Similarity NPC165447
0.5714 Remote Similarity NPC477723
0.5714 Remote Similarity NPC55383
0.5714 Remote Similarity NPC256656
0.5714 Remote Similarity NPC244038
0.5714 Remote Similarity NPC255042
0.5692 Remote Similarity NPC110732
0.569 Remote Similarity NPC304151
0.5672 Remote Similarity NPC11130
0.5667 Remote Similarity NPC140501
0.5667 Remote Similarity NPC175614
0.5667 Remote Similarity NPC160628
0.5667 Remote Similarity NPC276825
0.5667 Remote Similarity NPC76976
0.5645 Remote Similarity NPC471276
0.5645 Remote Similarity NPC153538
0.5645 Remote Similarity NPC125122
0.5645 Remote Similarity NPC471275
0.5645 Remote Similarity NPC471280
0.5634 Remote Similarity NPC206660
0.5625 Remote Similarity NPC68014
0.5625 Remote Similarity NPC471597
0.5604 Remote Similarity NPC167419
0.56 Remote Similarity NPC324638

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC104138 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6176 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6 Remote Similarity NPD4219 Approved
0.5932 Remote Similarity NPD860 Phase 2
0.5902 Remote Similarity NPD4220 Pre-registration
0.5667 Remote Similarity NPD4265 Approved
0.56 Remote Similarity NPD3212 Clinical (unspecified phase)

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data